Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1215 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0610469219 sf0610468220 6 10469219 2.14E-11 2.48E-06
vg0725376226 sf0725375232 7 25376226 1.17E-10 NA
vg0610429989 sf0610428990 6 10429989 1.44E-10 8.92E-07
vg0610473706 sf0610472707 6 10473706 2.52E-10 1.97E-06
vg1215178307 sf1215175643 12 15178307 3.24E-10 1.00E-06
vg0611960920 sf0611959921 6 11960920 4.69E-10 1.93E-06
vg0611960936 sf0611959937 6 11960936 5.32E-10 8.07E-07
vg0805546679 sf0805545682 8 5546679 1.34E-09 NA
vg1214822308 sf1214819649 12 14822308 1.61E-09 2.88E-07
vg0129598442 sf0129597397 1 29598442 1.30E-06 NA
vg1020189984 sf1020118466 10 20189984 NA 2.77E-06